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<a href="FeatureFinderAlgorithmMRM_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMMRM_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMMRM_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="FeatureFinderAlgorithm_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="ProductModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/ProductModel.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="EmgFitter1D_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgFitter1D.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="EmgModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgModel.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="SavitzkyGolayFilter_8h.html">OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="GaussFilter_8h.html">OpenMS/FILTERING/SMOOTHING/GaussFilter.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="SignalToNoiseEstimatorMeanIterative_8h.html">OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMeanIterative.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="LinearResampler_8h.html">OpenMS/FILTERING/TRANSFORMERS/LinearResampler.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <boost/math/special_functions/fpclassify.hpp></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#include <limits></span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> {</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType></div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html"> 73</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html">FeatureFinderAlgorithmMRM</a> :</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><PeakType, FeatureType>,</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  {</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a2f89be2feec82f5414aedc09e488420b"> 80</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">FeatureFinderAlgorithm<PeakType, FeatureType>::MapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a2f89be2feec82f5414aedc09e488420b">MapType</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#ae4e0f0c176662a323a6a64d29ff986dd"> 81</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MapType::SpectrumType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a4097a067534171488208ac7b101b5c0c"> 82</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">SpectrumType::FloatDataArrays</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::param_</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::features_</a>;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::ff_</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::defaults_</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::map_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">enum</span></div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  {</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaaf388fcb6d444ef59841ef549ca6ee0da"> 95</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaaf388fcb6d444ef59841ef549ca6ee0da">RT</a> = <a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">Peak2D::RT</a>,</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaa35008b046ec2687e53152082281d0867"> 96</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaa35008b046ec2687e53152082281d0867">MZ</a> = <a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">Peak2D::MZ</a></div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  };</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a655f6cc951b2ed0b71161df3275dfe3f"> 101</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a655f6cc951b2ed0b71161df3275dfe3f">FeatureFinderAlgorithmMRM</a>() :</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><<a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>, FeatureType>()</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  {</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"min_rt_distance"</span>, 10.0, <span class="stringliteral">"Minimal distance of MRM features in seconds."</span>);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">"min_rt_distance"</span>, 0.0);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"min_num_peaks_per_feature"</span>, 5, <span class="stringliteral">"Minimal number of peaks which are needed for a single feature"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"min_num_peaks_per_feature"</span>, 1);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"min_signal_to_noise_ratio"</span>, 2.0, <span class="stringliteral">"Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise."</span>);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">"min_signal_to_noise_ratio"</span>, 0);</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"write_debug_files"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"If set to true, for each feature a plot will be created, in the subdirectory 'debug'"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"write_debug_files"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"resample_traces"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"resample_traces"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"write_debuginfo"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"If set to true, debug messages are written, the output can be somewhat lengthy."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"write_debuginfo"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>();</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  }</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb"> 123</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">run</a>()</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  {</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="comment">//-------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">//General initialization</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">//-------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <a class="code" href="classOpenMS_1_1Map.html">Map<Size, Map<Size, std::vector<std::pair<DoubleReal, PeakType></a> > > > traces;</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <a class="code" href="classOpenMS_1_1SignalToNoiseEstimatorMeanIterative.html">SignalToNoiseEstimatorMeanIterative<RichPeakSpectrum></a> sne;</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <a class="code" href="classOpenMS_1_1LinearResampler.html">LinearResampler</a> resampler;</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="comment">// Split the whole map into traces (== MRM transitions)</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, traces.size(), <span class="stringliteral">"Finding features in traces."</span>);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> counter(0);</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">//typename Map<Size, Map<Size, std::vector<std::pair<DoubleReal, PeakType> > > >::const_iterator it1 = traces.begin();</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="comment">//typename Map<Size, std::vector<std::pair<DoubleReal, PeakType> > >::const_iterator it2;</span></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <a class="code" href="classdouble.html">DoubleReal</a> min_rt_distance(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"min_rt_distance"</span>));</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <a class="code" href="classdouble.html">DoubleReal</a> min_signal_to_noise_ratio(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"min_signal_to_noise_ratio"</span>));</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> min_num_peaks_per_feature(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"min_num_peaks_per_feature"</span>));</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feature_id(0);</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">bool</span> write_debuginfo(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"write_debuginfo"</span>).<a class="code" href="classOpenMS_1_1DataValue.html#a15274045457dcf54a03e7b417c9e7644">toBool</a>());</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">bool</span> write_debug_files(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"write_debug_files"</span>).<a class="code" href="classOpenMS_1_1DataValue.html#a15274045457dcf54a03e7b417c9e7644">toBool</a>());</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">bool</span> resample_traces(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"resample_traces"</span>).<a class="code" href="classOpenMS_1_1DataValue.html#a15274045457dcf54a03e7b417c9e7644">toBool</a>());</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  {</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  std::cerr << <span class="stringliteral">"Starting feature finding #chromatograms="</span> << <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().size() << <span class="stringliteral">", #spectra="</span> << <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() << std::endl;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  }</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keyword">typename</span> std::vector<MSChromatogram<ChromatogramPeak> >::const_iterator first_it = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().begin();</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">for</span> (; first_it != <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().end(); ++first_it)</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  {</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// throw the peaks into a "spectrum" where the m/z values are RTs in reality (more a chromatogram)</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> chromatogram;</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="comment">//typename std::vector<std::pair<DoubleReal, PeakType> >::const_iterator it3 = it2->second.begin();</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram<ChromatogramPeak>::const_iterator</a> it = first_it->begin(); it != first_it->end(); ++it)</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  {</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <a class="code" href="classOpenMS_1_1RichPeak1D.html">RichPeak1D</a> peak;</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(it->getRT());</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(it->getIntensity());</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  chromatogram.push_back(peak);</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  }</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// TODO</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="comment">// find presection of separated RTs of peaks;</span></div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="comment">// resampling to min distance?</span></div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// for each of the section, try to estimate S/N</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="comment">// find core regions and fit them</span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">if</span> (resample_traces)</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  {</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="comment">// resample the chromatogram, first find minimal distance and use this as resampling distance</span></div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <a class="code" href="classdouble.html">DoubleReal</a> min_distance(std::numeric_limits<DoubleReal>::max()), old_rt(0);</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">RichPeakSpectrum::ConstIterator</a> it = chromatogram.begin(); it != chromatogram.end(); ++it)</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  {</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  {</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  std::cerr << <span class="stringliteral">"CHROMATOGRAM: "</span> << it->getMZ() << <span class="stringliteral">" "</span> << it->getIntensity() << std::endl;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  }</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <a class="code" href="classdouble.html">DoubleReal</a> rt_diff = it->getMZ() - old_rt;</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">if</span> (rt_diff < min_distance && rt_diff > 0)</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  {</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  min_distance = rt_diff;</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  }</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  old_rt = it->getMZ();</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  }</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span> </div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  {</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  std::cerr << <span class="stringliteral">"Min_distance="</span> << min_distance << std::endl;</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  }</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordflow">if</span> (min_distance > 50 || chromatogram.size() < min_num_peaks_per_feature)</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  {</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  }</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> resampler_param(resampler.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  resampler_param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"spacing"</span>, min_distance);</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  resampler.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(resampler_param);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  resampler.<a class="code" href="classOpenMS_1_1LinearResampler.html#ab610fcc25c710938dccd156c33421773">raster</a>(chromatogram);</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  }</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="comment">// now smooth the data</span></div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <a class="code" href="classOpenMS_1_1GaussFilter.html">GaussFilter</a> filter;</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> filter_param(filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(filter_param);</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="comment">// calculate signal to noise levels</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> sn_chrom;</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> sne_param(sne.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="comment">// set window length to whole range, we expect only at most one signal</span></div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  {</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  std::cerr << <span class="stringliteral">"win_len m/z: "</span> << (chromatogram.end() - 1)->getMZ() << <span class="stringliteral">" "</span> << chromatogram.begin()->getMZ() << std::endl;</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  }</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  sne_param.setValue(<span class="stringliteral">"win_len"</span>, (chromatogram.end() - 1)->getMZ() - chromatogram.begin()->getMZ());</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> </div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordflow">if</span> ((<a class="code" href="classdouble.html">DoubleReal</a>)sne_param.getValue(<span class="stringliteral">"win_len"</span>) < 10e-4)</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  {</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  }</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  sne.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(sne_param);</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  sne.<a class="code" href="classOpenMS_1_1SignalToNoiseEstimator.html#a2fba92bbe2385c5e632a4a802b7e49ae">init</a>(chromatogram.begin(), chromatogram.end());</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  {</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  std::cerr << first_it->getPrecursor().getMZ() << <span class="stringliteral">" "</span> << first_it->getProduct().getMZ() << <span class="stringliteral">" "</span>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  }</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">RichPeakSpectrum::Iterator</a> sit = chromatogram.begin(); sit != chromatogram.end(); ++sit)</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  {</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <a class="code" href="classdouble.html">DoubleReal</a> sn(sne.<a class="code" href="classOpenMS_1_1SignalToNoiseEstimator.html#a504423b06b9d69e88d2ff68c9050889a">getSignalToNoise</a>(sit));</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  sit->setMetaValue(<span class="stringliteral">"SN"</span>, sn);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  {</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  std::cerr << sit->getMZ() << <span class="stringliteral">" "</span> << sit->getIntensity() << <span class="stringliteral">" "</span> << sn << std::endl;</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  }</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">if</span> (min_signal_to_noise_ratio == 0 || sn > min_signal_to_noise_ratio)</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  {</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  sn_chrom.push_back(*sit);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  }</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  }</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> </div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="comment">// now find sections in the chromatogram which have high s/n value</span></div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <a class="code" href="classdouble.html">DoubleReal</a> last_rt(0), this_rt(0);</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  std::vector<std::vector<DPosition<2> > > sections;</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">RichPeakSpectrum::Iterator</a> sit = sn_chrom.begin(); sit != sn_chrom.end(); ++sit)</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  {</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  {</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  std::cerr << <span class="stringliteral">"SECTIONS: "</span> << sit->getMZ() << <span class="stringliteral">" "</span> << sit->getIntensity() << std::endl;</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  }</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  this_rt = sit->getMZ();</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordflow">if</span> (sections.empty() || (this_rt - last_rt) > min_rt_distance)</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  {</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  std::cerr << <span class="stringliteral">"Starting new section, sections.size()="</span> << sections.size() << <span class="stringliteral">", rt_diff="</span> << this_rt - last_rt << std::endl;</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  }</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="comment">// new section</span></div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  std::vector<DPosition<2> > section;</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  section.push_back(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this_rt, sit->getIntensity()));</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  sections.push_back(section);</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  }</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  {</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  sections.back().push_back(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this_rt, sit->getIntensity()));</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  }</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  last_rt = this_rt;</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  }</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="comment">// for each of the sections identify local maxima which can be used for extension</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="comment">// if needed split the sections into smaller sections</span></div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i != sections.size(); ++i)</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  {</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">if</span> (sections[i].size() < min_num_peaks_per_feature)</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  {</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  }</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span> </div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  std::vector<DoubleReal> deltas(2, 0.0);</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <a class="code" href="classdouble.html">DoubleReal</a> last_int(sections[i][0].getY());</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 1; j < sections[i].size(); ++j)</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  {</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  deltas.push_back((sections[i][j].getY() - last_int) / last_int);</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  last_int = sections[i][j].getY();</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordflow">if</span> (write_debuginfo)</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  {</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <a class="code" href="classdouble.html">DoubleReal</a> average_delta = std::accumulate(deltas.begin(), deltas.end(), 0.0) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)3.0;</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  std::cerr << <span class="stringliteral">"AverageDelta: "</span> << average_delta << <span class="stringliteral">" ("</span> << sections[i][j].getX() << <span class="stringliteral">", "</span> << sections[i][j].getY() << <span class="stringliteral">")"</span> << std::endl;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  }</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  }</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  }</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span> </div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="comment">// for each section estimate the rt min/max and add up the intensities</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i != sections.size(); ++i)</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  {</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">if</span> (sections[i].size() > min_num_peaks_per_feature)</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="comment">// first smooth the data to prevent outliers from destroying the fit</span></div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> filter_spec;</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j != sections[i].size(); ++j)</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  {</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> p;</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(sections[i][j].getX());</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(sections[i][j].getY());</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  filter_spec.push_back(p);</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  }</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="comment">// add two peaks at the beginning and at the end for better fit</span></div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="comment">// therefore calculate average distance first</span></div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  std::vector<DoubleReal> distances;</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 1; j < filter_spec.size(); ++j)</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  {</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  distances.push_back(filter_spec[j].getMZ() - filter_spec[j - 1].getMZ());</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  }</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist_average = std::accumulate(distances.begin(), distances.end(), 0.0) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)distances.size();</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span> </div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="comment">// append peaks</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> new_peak;</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0);</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  filter_spec.push_back(new_peak);</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  filter_spec.push_back(new_peak);</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  filter_spec.push_back(new_peak);</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span> </div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="comment">// prepend peaks</span></div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  filter_spec.insert(filter_spec.begin(), new_peak);</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  filter_spec.insert(filter_spec.begin(), new_peak);</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  filter_spec.insert(filter_spec.begin(), new_peak);</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span> </div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  filter_param.setValue(<span class="stringliteral">"gaussian_width"</span>, 4 * dist_average);</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(filter_param);</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="comment">// smooth the data</span></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  filter.<a class="code" href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">filter</a>(filter_spec);</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> </div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="comment">// transform the data for fitting and fit RT profile</span></div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  std::vector<PeakType> data_to_fit;</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j != filter_spec.size(); ++j)</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  {</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a> p;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  p.<a class="code" href="classOpenMS_1_1Peak2D.html#abbdecccbbcf763c6c5eae3b7c3cb915e">setPosition</a>(filter_spec[j].getMZ());</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  p.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(filter_spec[j].getIntensity());</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  data_to_fit.push_back(p);</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  }</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * model_rt = 0;</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <a class="code" href="classdouble.html">DoubleReal</a> quality = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a59dd43367e76a334f8f481b100a275d0">fitRT_</a>(data_to_fit, model_rt);</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> </div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">setQuality</a>(0, quality);</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(quality);</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <a class="code" href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">ConvexHull2D::PointArrayType</a> hull_points(sections[i].size());</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <a class="code" href="classdouble.html">DoubleReal</a> intensity_sum(0.0), rt_sum(0.0);</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < sections[i].size(); ++j)</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  {</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  hull_points[j][0] = sections[i][j].getX();</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  hull_points[j][1] = first_it->getProduct().getMZ();</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span> </div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  rt_sum += sections[i][j].getX();</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  intensity_sum += sections[i][j].getY();</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  }</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span> </div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="comment">// create the feature according to fit</span></div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>((<a class="code" href="classdouble.html">DoubleReal</a>)model_rt-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"emg:retention"</span>));</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>((<a class="code" href="classdouble.html">DoubleReal</a>)first_it->getProduct().getMZ());</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(intensity_sum);</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <a class="code" href="classOpenMS_1_1ConvexHull2D.html">ConvexHull2D</a> hull;</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  hull.<a class="code" href="classOpenMS_1_1ConvexHull2D.html#ad84ba51670fc0bd9b6b2091ba27c3013">addPoints</a>(hull_points);</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().push_back(hull);</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">"MZ"</span>, (<a class="code" href="classdouble.html">DoubleReal</a>)first_it->getPrecursor().getMZ());</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span> </div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span> </div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <span class="comment">// add the model to the feature</span></div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html">ProductModel<2></a> prod_model;</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  prod_model.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a8cd14764d47842020930ef7023a2d912">setModel</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>, model_rt);</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a59f31f35e2e4a45316651cebbb358a1d">setModelDescription</a>(<a class="code" href="classOpenMS_1_1ModelDescription.html">ModelDescription<2></a>(&prod_model));</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span> </div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span> </div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  feature_id++;</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> </div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="comment">// writes a feature plot using gnuplot (should be installed on computer)</span></div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="keywordflow">if</span> (write_debug_files)</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  {</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> base_name = <span class="stringliteral">"debug/"</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>((<a class="code" href="classdouble.html">DoubleReal</a>)f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"MZ"</span>)) + <span class="stringliteral">"_id"</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(feature_id) + <span class="stringliteral">"_RT"</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>()) + <span class="stringliteral">"_Q3"</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(f.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>());</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  std::ofstream data_out(<a class="code" href="classOpenMS_1_1String.html">String</a>(base_name + <span class="stringliteral">"_data.dat"</span>).c_str());</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < sections[i].size(); ++j)</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  {</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <span class="comment">// RT intensity</span></div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <a class="code" href="classdouble.html">DoubleReal</a> rt = sections[i][j].getX();</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <a class="code" href="classdouble.html">DoubleReal</a> intensity = sections[i][j].getY();</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  data_out << rt << <span class="stringliteral">" "</span> << intensity << std::endl;</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  }</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  data_out.close();</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span> </div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  std::ofstream smoothed_data_out(<a class="code" href="classOpenMS_1_1String.html">String</a>(base_name + <span class="stringliteral">"_smoothed_data.dat"</span>).c_str());</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < filter_spec.size(); ++j)</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  {</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  smoothed_data_out << filter_spec[j].getMZ() + 0.5 << <span class="stringliteral">" "</span> << filter_spec[j].getIntensity() << std::endl;</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  }</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  smoothed_data_out.close();</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> </div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  std::ofstream fit_out(<a class="code" href="classOpenMS_1_1String.html">String</a>(base_name + <span class="stringliteral">"_rt_fit.dat"</span>).c_str());</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <a class="code" href="classOpenMS_1_1EmgModel.html">EmgModel</a> emg_model;</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  emg_model.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(model_rt-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  emg_model.<a class="code" href="classOpenMS_1_1EmgModel.html#a79142df18e1c10cc321e68ddb3ee72df">setSamples</a>();</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <a class="code" href="classdouble.html">DoubleReal</a> bb_min((<a class="code" href="classdouble.html">DoubleReal</a>)emg_model.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"bounding_box:min"</span>));</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <a class="code" href="classdouble.html">DoubleReal</a> bb_max((<a class="code" href="classdouble.html">DoubleReal</a>)emg_model.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"bounding_box:max"</span>));</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <a class="code" href="classdouble.html">DoubleReal</a> int_step((<a class="code" href="classdouble.html">DoubleReal</a>)emg_model.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"interpolation_step"</span>));</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">for</span> (<a class="code" href="classdouble.html">DoubleReal</a> pos = bb_min; pos < bb_max; pos += int_step)</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  {</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="comment">// RT intensity</span></div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  fit_out << pos << <span class="stringliteral">" "</span> << emg_model.<a class="code" href="classOpenMS_1_1InterpolationModel.html#ac4534e8323ba5dc157bc4bba75096d50">getIntensity</a>(pos) << std::endl;</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  }</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  fit_out.close();</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> </div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  std::ofstream gnuplot_out(<a class="code" href="classOpenMS_1_1String.html">String</a>(base_name + <span class="stringliteral">"_gnuplot.gpl"</span>).c_str());</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  gnuplot_out << <span class="stringliteral">"set terminal png"</span> << std::endl;</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  gnuplot_out << <span class="stringliteral">"set output \""</span> << base_name << <span class="stringliteral">".png\""</span> << std::endl;</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  gnuplot_out << <span class="stringliteral">"plot '"</span> << base_name << <span class="stringliteral">"_data.dat' w i, '"</span> << base_name << <span class="stringliteral">"_smoothed_data.dat' w i, '"</span> << base_name << <span class="stringliteral">"_rt_fit.dat' w lp title 'quality="</span> << f.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>() << <span class="stringliteral">"'"</span> << std::endl;</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  gnuplot_out.close();</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> gnuplot_call = <span class="stringliteral">"gnuplot "</span> + base_name + <span class="stringliteral">"_gnuplot.gpl"</span>;</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordtype">int</span> error = system(gnuplot_call.c_str());</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordflow">if</span> (error != 0)</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  {</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  std::cerr << <span class="stringliteral">"An error occurred during the gnuplot execution"</span> << std::endl;</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  }</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  }</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>->push_back(f);</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  }</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span> </div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++counter);</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  }</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  }</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span> </div>
<div class="line"><a name="l00446"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a81483ea6deb5aa7b6e11d0c3c871f532"> 446</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType></a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a>()</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  {</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a655f6cc951b2ed0b71161df3275dfe3f">FeatureFinderAlgorithmMRM</a>();</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  }</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span> </div>
<div class="line"><a name="l00451"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#af73fd15708e50e77665070023a09cc87"> 451</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  {</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordflow">return</span> <span class="stringliteral">"mrm"</span>;</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  }</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> </div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span> </div>
<div class="line"><a name="l00458"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a59dd43367e76a334f8f481b100a275d0"> 458</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a59dd43367e76a334f8f481b100a275d0">fitRT_</a>(std::vector<PeakType> & rt_input_data, <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * & model)<span class="keyword"> const</span></div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <a class="code" href="classdouble.html">DoubleReal</a> quality;</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> param;</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <a class="code" href="classOpenMS_1_1EmgFitter1D.html">EmgFitter1D</a> fitter;</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span> </div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span> <span class="comment">param.setValue( "tolerance_stdev_bounding_box", tolerance_stdev_box_);</span></div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span> <span class="comment">param.setValue( "statistics:mean", rt_stat_.mean() );</span></div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span> <span class="comment">param.setValue( "statistics:variance", rt_stat_.variance() );</span></div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span> <span class="comment">param.setValue( "interpolation_step", interpolation_step_rt_ );</span></div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> <span class="comment">param.setValue( "max_iteration", max_iteration_);</span></div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span> <span class="comment">param.setValue( "deltaAbsError", deltaAbsError_);</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> <span class="comment">param.setValue( "deltaRelError", deltaRelError_);</span></div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span> </div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="comment">// Set parameter for fitter</span></div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  fitter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span> </div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="comment">// Construct model for rt</span></div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  quality = fitter.<a class="code" href="classOpenMS_1_1EmgFitter1D.html#a250458ea3a48557d8a6ccaa2df1ee1ec">fit1d</a>(rt_input_data, model);</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span> </div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="comment">// Check quality</span></div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordflow">if</span> (boost::math::isnan(quality)) quality = -1.0;</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span> </div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keywordflow">return</span> quality;</div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  }</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span> </div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  <span class="comment">//Docu in base class</span></div>
<div class="line"><a name="l00487"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a776f7572fc4f466e9527ca233471920d"> 487</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  {</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  }</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span> </div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  };</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span> </div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span> </div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMMRM_H</span></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue & getMetaValue(const String &name) const </div><div class="ttdoc">returns the value corresponding to a string </div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseEstimator_html_a504423b06b9d69e88d2ff68c9050889a"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimator.html#a504423b06b9d69e88d2ff68c9050889a">OpenMS::SignalToNoiseEstimator::getSignalToNoise</a></div><div class="ttdeci">virtual double getSignalToNoise(const PeakIterator &data_point)</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimator.h:130</div></div>
<div class="ttc" id="ProductModel_8h_html"><div class="ttname"><a href="ProductModel_8h.html">ProductModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html_a8cd14764d47842020930ef7023a2d912"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html#a8cd14764d47842020930ef7023a2d912">OpenMS::ProductModel< 2 >::setModel</a></div><div class="ttdeci">ProductModel & setModel(UInt dim, BaseModel< 1 > *dist)</div><div class="ttdoc">set model dist for dimension dim </div><div class="ttdef"><b>Definition:</b> ProductModel.h:184</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &name, const DataValue &value)</div><div class="ttdoc">sets the DataValue corresponding to a name </div></div>
<div class="ttc" id="classOpenMS_1_1EmgModel_html"><div class="ttname"><a href="classOpenMS_1_1EmgModel.html">OpenMS::EmgModel</a></div><div class="ttdoc">Exponentially modified gaussian distribution model for elution profiles. </div><div class="ttdef"><b>Definition:</b> EmgModel.h:50</div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeatureFinderAlgorithm::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a761b1937850c141d0c6fff0e4d633a04"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">OpenMS::DefaultParamHandler::defaults_</a></div><div class="ttdeci">Param defaults_</div><div class="ttdoc">Container for default parameters. This member should be filled in the constructor of derived classes!...</div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1LinearResampler_html"><div class="ttname"><a href="classOpenMS_1_1LinearResampler.html">OpenMS::LinearResampler</a></div><div class="ttdoc">Linear Resampling of raw data. </div><div class="ttdef"><b>Definition:</b> LinearResampler.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeatureFinderAlgorithm::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html">OpenMS::Peak2D</a></div><div class="ttdoc">A 2-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html">OpenMS::FeatureFinderAlgorithmMRM</a></div><div class="ttdoc">FeatureFinderAlgorithm for MRM experiments. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a0adf747960bee685e34bfbbe57a7089b"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">OpenMS::Feature::getOverallQuality</a></div><div class="ttdeci">QualityType getOverallQuality() const </div><div class="ttdoc">Non-mutable access to the overall quality. </div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a></div><div class="ttdoc">The representation of a chromatogram. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeatureFinderAlgorithm::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a2f89be2feec82f5414aedc09e488420b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a2f89be2feec82f5414aedc09e488420b">OpenMS::FeatureFinderAlgorithmMRM::MapType</a></div><div class="ttdeci">FeatureFinderAlgorithm< PeakType, FeatureType >::MapType MapType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">OpenMS::Peak2D::RT</a></div><div class="ttdoc">Retention time dimension id (0 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_abdcce0f11b8d73a2b4da5b1a00457d7b"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">OpenMS::ConvexHull2D::PointArrayType</a></div><div class="ttdeci">std::vector< PointType > PointArrayType</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html">OpenMS::FeatureFinderAlgorithm</a></div><div class="ttdoc">Abstract base class for FeatureFinder algorithms. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a4895afe86c2aa0747ae0411c58c82114"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">OpenMS::MSSpectrum< RichPeak1D >::ConstIterator</a></div><div class="ttdeci">ContainerType::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:125</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_ae4e0f0c176662a323a6a64d29ff986dd"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#ae4e0f0c176662a323a6a64d29ff986dd">OpenMS::FeatureFinderAlgorithmMRM::SpectrumType</a></div><div class="ttdeci">MapType::SpectrumType SpectrumType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:81</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1EmgFitter1D_html"><div class="ttname"><a href="classOpenMS_1_1EmgFitter1D.html">OpenMS::EmgFitter1D</a></div><div class="ttdoc">Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL...</div><div class="ttdef"><b>Definition:</b> EmgFitter1D.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">OpenMS::Peak2D::MZ</a></div><div class="ttdoc">Mass-to-charge dimension id (1 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1EmgFitter1D_html_a250458ea3a48557d8a6ccaa2df1ee1ec"><div class="ttname"><a href="classOpenMS_1_1EmgFitter1D.html#a250458ea3a48557d8a6ccaa2df1ee1ec">OpenMS::EmgFitter1D::fit1d</a></div><div class="ttdeci">QualityType fit1d(const RawDataArrayType &range, InterpolationModel *&model)</div><div class="ttdoc">return interpolation model </div></div>
<div class="ttc" id="GaussFilter_8h_html"><div class="ttname"><a href="GaussFilter_8h.html">GaussFilter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a59f31f35e2e4a45316651cebbb358a1d"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a59f31f35e2e4a45316651cebbb358a1d">OpenMS::Feature::setModelDescription</a></div><div class="ttdeci">void setModelDescription(const ModelDescription< 2 > &q)</div><div class="ttdoc">Set the model description. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab4e0f356f837ce58e57695da114adce3"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">OpenMS::Peak2D::getRT</a></div><div class="ttdeci">CoordinateType getRT() const </div><div class="ttdoc">Returns the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html">OpenMS::ProductModel< 2 ></a></div><div class="ttdoc">The class template is only implemented for D=2 because we use Peak2D here. </div><div class="ttdef"><b>Definition:</b> ProductModel.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak1D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak1D.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1RichPeak1D_html"><div class="ttname"><a href="classOpenMS_1_1RichPeak1D.html">OpenMS::RichPeak1D</a></div><div class="ttdoc">A 1-dimensional raw data point or peak mith meta information. </div><div class="ttdef"><b>Definition:</b> RichPeak1D.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a6d64276a665c3c0dca8fb4ade3c8b477"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">OpenMS::MSSpectrum< RichPeak1D >::Iterator</a></div><div class="ttdeci">ContainerType::iterator Iterator</div><div class="ttdoc">Mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html">OpenMS::ConvexHull2D</a></div><div class="ttdoc">A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling...</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:75</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html">OpenMS::FeatureFinderDefs</a></div><div class="ttdoc">The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a59dd43367e76a334f8f481b100a275d0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a59dd43367e76a334f8f481b100a275d0">OpenMS::FeatureFinderAlgorithmMRM::fitRT_</a></div><div class="ttdeci">DoubleReal fitRT_(std::vector< PeakType > &rt_input_data, InterpolationModel *&model) const </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:458</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak2D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Non-mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_ae2fc906f686ab141e88c57655afd1774"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">OpenMS::MSSpectrum< PeakType >::FloatDataArrays</a></div><div class="ttdeci">std::vector< FloatDataArray > FloatDataArrays</div><div class="ttdoc">Float data array vector type. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a80155586fa275b28773c9b203f52cabaaf388fcb6d444ef59841ef549ca6ee0da"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaaf388fcb6d444ef59841ef549ca6ee0da">OpenMS::FeatureFinderAlgorithmMRM::RT</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1InterpolationModel_html"><div class="ttname"><a href="classOpenMS_1_1InterpolationModel.html">OpenMS::InterpolationModel</a></div><div class="ttdoc">Abstract class for 1D-models that are approximated using linear interpolation. </div><div class="ttdef"><b>Definition:</b> InterpolationModel.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseEstimatorMeanIterative_html"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimatorMeanIterative.html">OpenMS::SignalToNoiseEstimatorMeanIterative</a></div><div class="ttdoc">Estimates the signal/noise (S/N) ratio of each data point in a scan based on an iterative scheme whic...</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimatorMeanIterative.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseEstimator_html_a2fba92bbe2385c5e632a4a802b7e49ae"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimator.html#a2fba92bbe2385c5e632a4a802b7e49ae">OpenMS::SignalToNoiseEstimator::init</a></div><div class="ttdeci">virtual void init(const PeakIterator &it_begin, const PeakIterator &it_end)</div><div class="ttdoc">Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimator.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1InterpolationModel_html_ac4534e8323ba5dc157bc4bba75096d50"><div class="ttname"><a href="classOpenMS_1_1InterpolationModel.html#ac4534e8323ba5dc157bc4bba75096d50">OpenMS::InterpolationModel::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity(const PositionType &pos) const </div><div class="ttdoc">access model predicted intensity at position pos </div><div class="ttdef"><b>Definition:</b> InterpolationModel.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector< ConvexHull2D > & getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a93cd3fc199fc903768e3b8d7fafaeb95"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">OpenMS::Feature::setQuality</a></div><div class="ttdeci">void setQuality(Size index, QualityType q)</div><div class="ttdoc">Set the quality in dimension c. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a4097a067534171488208ac7b101b5c0c"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a4097a067534171488208ac7b101b5c0c">OpenMS::FeatureFinderAlgorithmMRM::FloatDataArrays</a></div><div class="ttdeci">SpectrumType::FloatDataArrays FloatDataArrays</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html">OpenMS::Peak1D</a></div><div class="ttdoc">A 1-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a655f6cc951b2ed0b71161df3275dfe3f"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a655f6cc951b2ed0b71161df3275dfe3f">OpenMS::FeatureFinderAlgorithmMRM::FeatureFinderAlgorithmMRM</a></div><div class="ttdeci">FeatureFinderAlgorithmMRM()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
<div class="ttc" id="FeatureFinderAlgorithm_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm_8h.html">FeatureFinderAlgorithm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_abbdecccbbcf763c6c5eae3b7c3cb915e"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#abbdecccbbcf763c6c5eae3b7c3cb915e">OpenMS::Peak2D::setPosition</a></div><div class="ttdeci">void setPosition(const PositionType &position)</div><div class="ttdoc">Mutable access to the position. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a776f7572fc4f466e9527ca233471920d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a776f7572fc4f466e9527ca233471920d">OpenMS::FeatureFinderAlgorithmMRM::updateMembers_</a></div><div class="ttdeci">virtual void updateMembers_()</div><div class="ttdoc">This method is used to update extra member variables at the end of the setParameters() method...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:487</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a72fcb26a14f6beb1c3fbace9ab3e7dbb"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">OpenMS::FeatureFinderAlgorithmMRM::run</a></div><div class="ttdeci">virtual void run()</div><div class="ttdoc">Main method for actual FeatureFinder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a10933782584a46cded91c40574027ee2"><div class="ttname"><a href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">OpenMS::Param::setValidStrings</a></div><div class="ttdeci">void setValidStrings(const String &key, const std::vector< String > &strings)</div><div class="ttdoc">Sets the valid strings for the parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak2D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Returns the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:191</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="EmgFitter1D_8h_html"><div class="ttname"><a href="EmgFitter1D_8h.html">EmgFitter1D.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html">OpenMS::GaussFilter</a></div><div class="ttdoc">This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...</div><div class="ttdef"><b>Definition:</b> GaussFilter.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ModelDescription_html"><div class="ttname"><a href="classOpenMS_1_1ModelDescription.html">OpenMS::ModelDescription< 2 ></a></div></div>
<div class="ttc" id="SavitzkyGolayFilter_8h_html"><div class="ttname"><a href="SavitzkyGolayFilter_8h.html">SavitzkyGolayFilter.h</a></div></div>
<div class="ttc" id="EmgModel_8h_html"><div class="ttname"><a href="EmgModel_8h.html">EmgModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_aeba0cded976431f70fbea5499218ce18"><div class="ttname"><a href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">OpenMS::Feature::setOverallQuality</a></div><div class="ttdeci">void setOverallQuality(QualityType q)</div><div class="ttdoc">Set the overall quality. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a3a23089ec40eeed796efe7b69ecb02ac"><div class="ttname"><a href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">OpenMS::Param::setMinInt</a></div><div class="ttdeci">void setMinInt(const String &key, Int min)</div><div class="ttdoc">Sets the minimum value for the integer or integer list parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1LinearResampler_html_ab610fcc25c710938dccd156c33421773"><div class="ttname"><a href="classOpenMS_1_1LinearResampler.html#ab610fcc25c710938dccd156c33421773">OpenMS::LinearResampler::raster</a></div><div class="ttdeci">void raster(MSSpectrum< PeakType > &spectrum)</div><div class="ttdoc">Applies the resampling algorithm to an MSSpectrum. </div><div class="ttdef"><b>Definition:</b> LinearResampler.h:85</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af1c45ecd71b5041b70319249e8e73591"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">OpenMS::ProgressLogger::startProgress</a></div><div class="ttdeci">void startProgress(SignedSize begin, SignedSize end, const String &label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a15274045457dcf54a03e7b417c9e7644"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a15274045457dcf54a03e7b417c9e7644">OpenMS::DataValue::toBool</a></div><div class="ttdeci">bool toBool() const </div><div class="ttdoc">Conversion to bool. </div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a8852277abd03220cc7b80d6c1bed6fed"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">OpenMS::ProgressLogger::setProgress</a></div><div class="ttdeci">void setProgress(SignedSize value) const </div><div class="ttdoc">Sets the current progress. </div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_ad84ba51670fc0bd9b6b2091ba27c3013"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#ad84ba51670fc0bd9b6b2091ba27c3013">OpenMS::ConvexHull2D::addPoints</a></div><div class="ttdeci">void addPoints(const PointArrayType &points)</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a80155586fa275b28773c9b203f52cabaa35008b046ec2687e53152082281d0867"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a80155586fa275b28773c9b203f52cabaa35008b046ec2687e53152082281d0867">OpenMS::FeatureFinderAlgorithmMRM::MZ</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:96</div></div>
<div class="ttc" id="SignalToNoiseEstimatorMeanIterative_8h_html"><div class="ttname"><a href="SignalToNoiseEstimatorMeanIterative_8h.html">SignalToNoiseEstimatorMeanIterative.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#af73fd15708e50e77665070023a09cc87">OpenMS::FeatureFinderAlgorithmMRM::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:451</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmMRM_html_a81483ea6deb5aa7b6e11d0c3c871f532"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmMRM.html#a81483ea6deb5aa7b6e11d0c3c871f532">OpenMS::FeatureFinderAlgorithmMRM::create</a></div><div class="ttdeci">static FeatureFinderAlgorithm< PeakType, FeatureType > * create()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmMRM.h:446</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_aadc7a8536eb15f8c6fa05eefca0e25be"><div class="ttname"><a href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">OpenMS::Param::setMinFloat</a></div><div class="ttdeci">void setMinFloat(const String &key, DoubleReal min)</div><div class="ttdoc">Sets the minimum value for the floating point or floating point list parameter key. </div></div>
<div class="ttc" id="LinearResampler_8h_html"><div class="ttname"><a href="LinearResampler_8h.html">LinearResampler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_ab978eb8c2316573b1753199c8af2b041"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">OpenMS::GaussFilter::filter</a></div><div class="ttdeci">void filter(MSSpectrum< PeakType > &spectrum)</div><div class="ttdoc">Smoothes an MSSpectrum containing profile data. </div><div class="ttdef"><b>Definition:</b> GaussFilter.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a7f6aab5a7dfbdd1c062a4352a29361f3"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">OpenMS::DefaultParamHandler::getParameters</a></div><div class="ttdeci">const Param & getParameters() const </div><div class="ttdoc">Non-mutable access to the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1EmgModel_html_a79142df18e1c10cc321e68ddb3ee72df"><div class="ttname"><a href="classOpenMS_1_1EmgModel.html#a79142df18e1c10cc321e68ddb3ee72df">OpenMS::EmgModel::setSamples</a></div><div class="ttdeci">void setSamples()</div><div class="ttdoc">set sample/supporting points of interpolation </div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a02fccfed86a20f8bd0f6b98c23fadb2e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">OpenMS::MSExperiment::getChromatograms</a></div><div class="ttdeci">const std::vector< MSChromatogram< ChromatogramPeakType > > & getChromatograms() const </div><div class="ttdoc">returns the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:768</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a2802c591e6d7fd3fd9cc35f5e875d0ba"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">OpenMS::DefaultParamHandler::defaultsToParam_</a></div><div class="ttdeci">void defaultsToParam_()</div><div class="ttdoc">Updates the parameters after the defaults have been set in the constructor. </div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
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